R SIG Fedora - Mar 2024 - evince not showing "greek" and "math" in *.pdf plots

Martin, I wouldn't rule out an R issue yet. Fonts are... tricky. So I'm
cc'ing Paul Murrell here.

I tried several viewers here and I see the following: Chrome, Firefox and
Libreoffice Draw show the symbols; however, evince, okular and xournal++
agree on **not** showing the symbols. **If** there is a bug, the bug would
be in fontconfig, because these ones AFAIK properly delegate on fontconfig,
which is the system-wide component that decides what font substitution
should be made for any given font. However, I see:

$ fc-match Helvetica
NimbusSans-Regular.otf: "Nimbus Sans" "Regular"

which is the right choice. And okular confirms this by showing in a
properties dialog that it is substituting Helvetica with URW's Nimbus Sans
Regular. So why aren't the symbols displayed? My best guess is that this
has something to do with how R encodes such symbols. Paul introduced some
changes to fix similar issues for Cairo devices when Fedora dropped support
for Type 1 fonts, see [1]. Now, I'm no font expert, but it seems to me that
the pdf device may require similar fixes. (And why do xpdf or Firefox show
the glyphs... I have no idea. I guess they do their thing without asking
fontconfig).

[1]
https://blog.r-project.org/2020/04/17/changes-to-symbol-fonts-for-cairo-graphics-devices/

Peter, as an aside, note that cairo_pdf embeds the fonts by default.

Best,
I?aki

On Mon, 11 Mar 2024 at 15:31, <pstils at gmail.com> wrote:
> Hi Martin and Tim,
>
> I also have this bug. Though I think not necessarily with all the same
> fonts as Martin.
>
> Using Martin's code:
>
> https://imgur.com/a/ILUoe3H
>
> Fedora 39, Evince 45.0
>
> It's a bug with Evince. I think. I think it's substituting in a
font
> set that doesn't have all the required symbols. I think it should be
> possible to install the required fonts, but I haven't found a solution
> that way, yet.
>
> Nevertheless, the following should work, and may be a better solution
> anyway, given that embedding the fonts is probably more cross-
> platform/viewer friendly:
>
>
> You can embed the fonts if you have Ghostscript installed (I think it
> comes with Fedora already(?) if not then:
>
> sudo dnf install ghostscript
>
> )
>
>
> You can then use the embedFonts() function in R:
>
> (pdfil <- paste0("plotmath-example_R",
>                  with(R.version, paste0(major, sub("[.]",
"", minor))),
> ".pdf"))
>
> pdf(pdfil)
> example(plotmath); mtext(R.version.string)
> dev.off()
>
> # Use embedFonts to embed the fonts in the PDF
> embedFonts(file = pdfil, outfile = paste0("embedded-example",
pdfil),
> options = "-dPDFSETTINGS=/prepress")
>
>
> if(interactive()) {
>   system(paste("evince", paste0("embedded-example",
pdfil), "&"))
> }
>
>
>
> Or you can do it in the terminal:
>
>
> gs -dNOPAUSE -dBATCH -dPDFSETTINGS=/prepress -sDEVICE=pdfwrite -
> dEmbedAllFonts=true -sOutputFile=plotmath-example-output_embedded.pdf -
> f plotmath-example_R432.pdf
>
>
> Compare:
>
>
> Embedded:
>
> ? pdffonts plotmath-example-output_embedded.pdf
> name                   type     encoding emb sub uni object ID
> ---------------------- -------- -------- --- --- --- ------ ---
> KHEPSB+Helvetica       Type 1C  Custom   yes yes no      10   0
> WNPVSJ+Symbol          Type 1C  Custom   yes yes no      12   0
> MQBKOK+Helvetica-Bold  Type 1C  WinAnsi  yes yes no      20   0
>
>
> Original:
>
> ? pdffonts plotmath-example_R432.pdf
> name                   type     encoding emb sub uni object ID
> ---------------------- -------- -------- --- --- --- ------ ---
> Helvetica              Type 1   Custom   no  no  no      16  0
> Helvetica-Bold         Type 1   Custom   no  no  no      17  0
> Symbol                 Type 1   Symbol   no  no  no      18  0
>
>
> I hope this works for you. Like I said, I *think* it's a problem with
> Evince so it's probably better to file a bug report with them, but I
> also think embedding fonts isn't such a bad idea anyway - you'll
know
> the output will display as intended regardless of the viewer on the
> user's system. It does lead to a larger file-size, but I think these
> days we can live with that.
>
> Thanks,
> Peter
>
>
>
>
> On Mon, 2024-03-11 at 14:15 +0100, Martin Maechler wrote:
> > > > > > > Tim Taylor
> > > > > > >     on Mon, 11 Mar 2024 11:42:35 +0000
writes:
> >
> >     > Hi Martin
> >     > Probably not the answer you're looking for but on the
latest
> > Fedora 39 (workstation edition) both locally, and on a freshly
> > installed VM (with just R-core installed), all fonts render correctly
> > for me in evince.
> >
> >     > $ evince --version
> >     > GNOME Document Viewer 45.0
> >
> >     > $ R --version
> >     > R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
> >     > Copyright (C) 2024 The R Foundation for Statistical Computing
> >     > Platform: x86_64-redhat-linux-gnu (64-bit)
> >
> >     > It may be worth sharing more details about your installation
> > (e.g. Fedora version) to see if anyone has any ideas.
> >
> >     > Tim
> >
> > Thank you, Tim.
> >
> >
> > Fedora is 38 :
> >
> > $ lsb_release -a
> > LSB Version:  :core-5.0-amd64:core-5.0-noarch:cxx-5.0-amd64:cxx-
> > 5.0-noarch:desktop-5.0-amd64:desktop-5.0-noarch:languages-5.0-
> > amd64:languages-5.0-noarch:printing-5.0-amd64:printing-5.0-noarch
> > Distributor ID:       Fedora
> > Description:  Fedora release 38 (Thirty Eight)
> > Release:      38
> > Codename:     ThirtyEight
> >
> > $ evince --version
> > GNOME Document Viewer 44.3
> >
> > R version does not matter at all.
> > Same phenomenon in several versions of R I have installed
> > simultaneously (from source).
> > As I mentioned, I'm slightly misusing the list for non-R problem
> > that I encounter a lot with R  {because I like to use
> > "plotmath"}, so I apologize in advance.
> >
> > Maybe it's rather a matter of fonts installed in
> > /usr/share/fonts/ ??
> >
> > Martin
> >
> >     > On Mon, 11 Mar 2024, at 10:51 AM, Martin Maechler wrote:
> >     >> This problem has bugged me for several years now,
> >     >> and our own IT staff has tried a few things, but then
never
> >     >> cared enough to persist fixing it.
> >     >>
> >     >> It *is* a bug in evince, the standard pdf viewer on
Fedora and
> >     >> IIUC also quite few other Linux distributions, and
> >     >> *not* a bug in R;  hence I am asking for help/hints here.
> >     >>
> >     >> A very simple example:
> >     >>
> >     >>
--------------------------------------------------------------
> > -----------------
> >     >>
> >     >> (pdfil <- paste0("plotmath-example_R",
> >     >> with(R.version, paste0(major, sub("[.]",
"", minor))),
> > ".pdf"))
> >     >> ## "plomath-example_R433.pdf"
> >     >>
> >     >> pdf(pdfil)
> >     >> example(plotmath); mtext(R.version.string)
> >     >> dev.off()
> >     >>
> >     >> if(interactive())
> >     >> system(paste("evince", pdfil,
"&"))
> >     >>
> >     >>
--------------------------------------------------------------
> > -----------------
> >     >>
> >     >> The pdf contains 4 pages, and in all of them *some* of
the
> > math
> >     >> symbols are replaced by open rectangles -- because evince
does
> >     >> not find the fonts it should.
> >     >>
> >     >> E.g.
> >     >> - page 1: \pi is properly shown,  \phi not
> >     >> - page 2: all greek letters,  \theta, \xi, \eta  are
*not*
> > shown
> >     >> ...
> >     >>
> >     >> Simply typing
> >     >>
> >     >> example(plotmath)
> >     >>
> >     >> in the R console will show you everything as it should be
but
> > is
> >     >> not for us, using evince.
> >     >>
> >     >> However, *everything* is rendered correctly, if I use
very old
> >     >> 'xpdf' {which you may have to install
> >     >>
> >     >> ## OTOH: This always work fine with the very old 
'xpdf' :
> >     >> system(paste("xpdf", pdfil, "&"))
> >     >>
> >     >> So the fonts *are* somewhere on my machine, but evince
does
> > not
> >     >> find them;
> >     >>
> >     >> How should our IT people fix this?
> >     >>
> >     >> IIRC they did install the Zapf Dingbats fonts -- which
then
> > are
> >     >> found by xpdf but not by evince ?
> >     >>
> >     >>
> >     >> Thank you in advance,
> >     >> Martin
> >     >>
> >     >> _______________________________________________
> >     >> R-SIG-Fedora mailing list
> >     >> R-SIG-Fedora at r-project.org
> >     >> https://stat.ethz.ch/mailman/listinfo/r-sig-fedora
> >     >>
> >
> >     > [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > R-SIG-Fedora mailing list
> > R-SIG-Fedora at r-project.org
> > https://stat.ethz.ch/mailman/listinfo/r-sig-fedora
>
> _______________________________________________
> R-SIG-Fedora mailing list
> R-SIG-Fedora at r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-fedora
>

-- 
I?aki ?car

	[[alternative HTML version deleted]]

HI I?aki,?

That's interesting.?

I may be wrong but I think it's the Symbol font that's got the
substitution bug, not Helvetica.?

? fc-match "Symbol"
StandardSymbolsPS.t1: "Standard Symbols PS" "Regular"

Is what I get, but then in the Evince properties it's telling me that
it's substituting Symbol with "Noto Sans Regular", despite the
Standard
Symbols PS font being installed.?


When I make a ~/.font.config file (I didn't have one already) with the
contents:?

<?xml version="1.0"?>
<!DOCTYPE fontconfig SYSTEM "fonts.dtd">
<fontconfig>

  <match target="pattern">
    <test name="family" qual="any" >
      <string>Symbol</string>
    </test>
    <edit name="family" mode="assign"
binding="same">
      <string>OpenSymbol</string>
    </edit>
  </match>

</fontconfig>


(OpenSymbol is in libreoffice-opensymbol-fonts)?


Then evince shows me the symbols. (Whether they're the correct ones or
not, I don't know! They look right to me, but I'm a biologist, so...).
?

And now:?

? fc-match "Symbol"
opens___.ttf: "OpenSymbol" "Regular"


So, I think that's another option for you, Martin. But I think
embedding might still be the better choice, anyway.?

I now don't think the bug is with Evince. I suspect something's?telling
Evince (and Okular) to use the wrong font, but you can force a more
appropriate substitution.


Do you think it could be this?:?

https://bugzilla.redhat.com/show_bug.cgi?id=2088665


Thanks,?
Peter

?



On Mon, 2024-03-11 at 18:59 +0100, I?aki Ucar wrote:
> Martin, I wouldn't rule out an R issue yet. Fonts are... tricky. So
> I'm cc'ing Paul Murrell here.?
> 
> I tried several?viewers here and I see the following: Chrome, Firefox
> and Libreoffice Draw show the symbols; however, evince, okular and
> xournal++ agree on **not** showing the symbols. **If** there is a
> bug, the bug would be in fontconfig, because these ones AFAIK
> properly delegate on fontconfig, which is the system-wide component
> that decides what font substitution should be made for any given
> font. However, I see:
> 
> $ fc-match Helvetica
> NimbusSans-Regular.otf: "Nimbus Sans" "Regular"
> 
> which is the right choice. And okular confirms this by showing in a
> properties dialog that it is substituting Helvetica with URW's Nimbus
> Sans Regular. So why aren't the symbols displayed? My best guess is
> that this has something to do with how R encodes such symbols. Paul
> introduced some changes to fix similar issues for Cairo devices when
> Fedora dropped support for Type 1 fonts, see [1]. Now, I'm no font
> expert, but it seems to me that the pdf device may require similar
> fixes. (And why do xpdf or Firefox show the glyphs... I have no idea.
> I guess they do their?thing without asking fontconfig).
> 
> [1]?https://blog.r-project.org/2020/04/17/changes-to-symbol-fonts-
> for-cairo-graphics-devices/
> 
> Peter, as an aside, note that cairo_pdf embeds the fonts by default.
> 
> Best,
> I?aki
> 
> On Mon, 11 Mar 2024 at 15:31, <pstils at gmail.com> wrote:
> > Hi Martin and Tim, 
> > 
> > I also have this bug. Though I think not necessarily with all the
> > same
> > fonts as Martin. 
> > 
> > Using Martin's code:
> > 
> > https://imgur.com/a/ILUoe3H
> > 
> > Fedora 39, Evince 45.0
> > 
> > It's a bug with Evince. I think. I think it's substituting in
a
> > font
> > set that doesn't have all the required symbols. I think it should
> > be
> > possible to install the required fonts, but I haven't found a
> > solution
> > that way, yet.?
> > 
> > Nevertheless, the following should work, and may be a better
> > solution
> > anyway, given that embedding the fonts is probably more cross-
> > platform/viewer friendly: 
> > 
> > 
> > You can embed the fonts if you have Ghostscript installed (I think
> > it
> > comes with Fedora already(?) if not then:?
> > 
> > sudo dnf install ghostscript 
> > 
> > )
> > 
> > 
> > You can then use the embedFonts() function in R:
> > 
> > (pdfil <- paste0("plotmath-example_R",
> > ? ? ? ? ? ? ? ? ?with(R.version, paste0(major, sub("[.]",
"",
> > minor))),
> > ".pdf"))
> > 
> > pdf(pdfil)
> > example(plotmath); mtext(R.version.string)
> > dev.off()
> > 
> > # Use embedFonts to embed the fonts in the PDF
> > embedFonts(file = pdfil, outfile =
paste0("embedded-example",
> > pdfil),
> > options = "-dPDFSETTINGS=/prepress")
> > 
> > 
> > if(interactive()) {
> > ? system(paste("evince",
paste0("embedded-example", pdfil), "&"))
> > }
> > 
> > 
> > 
> > Or you can do it in the terminal:
> > 
> > 
> > gs -dNOPAUSE -dBATCH -dPDFSETTINGS=/prepress -sDEVICE=pdfwrite -
> > dEmbedAllFonts=true -sOutputFile=plotmath-example-
> > output_embedded.pdf -
> > f plotmath-example_R432.pdf 
> > 
> > 
> > Compare: 
> > 
> > 
> > Embedded:
> > 
> > ? pdffonts plotmath-example-output_embedded.pdf
> > name? ? ? ? ? ? ? ? ? ?type? ? ?encoding emb sub uni object ID
> > ---------------------- -------- -------- --- --- --- ------ ---
> > KHEPSB+Helvetica? ? ? ?Type 1C? Custom? ?yes yes no? ? ? 10? ?0
> > WNPVSJ+Symbol? ? ? ? ? Type 1C? Custom? ?yes yes no? ? ? 12? ?0
> > MQBKOK+Helvetica-Bold? Type 1C? WinAnsi? yes yes no? ? ? 20? ?0
> > 
> > 
> > Original:
> > 
> > ? pdffonts plotmath-example_R432.pdf
> > name? ? ? ? ? ? ? ? ? ?type? ? ?encoding emb sub uni object ID
> > ---------------------- -------- -------- --- --- --- ------ ---
> > Helvetica? ? ? ? ? ? ? Type 1? ?Custom? ?no? no? no? ? ? 16? 0
> > Helvetica-Bold? ? ? ? ?Type 1? ?Custom? ?no? no? no? ? ? 17? 0
> > Symbol? ? ? ? ? ? ? ? ?Type 1? ?Symbol? ?no? no? no? ? ? 18? 0
> > 
> > 
> > I hope this works for you. Like I said, I *think* it's a problem
> > with
> > Evince so it's probably better to file a bug report with them, but
> > I
> > also think embedding fonts isn't such a bad idea anyway -
you'll
> > know
> > the output will display as intended regardless of the viewer on the
> > user's system. It does lead to a larger file-size, but I think
> > these
> > days we can live with that.
> > 
> > Thanks, 
> > Peter
> > 
> > 
> > 
> > 
> > On Mon, 2024-03-11 at 14:15 +0100, Martin Maechler wrote:
> > > > > > > > Tim Taylor 
> > > > > > > > ??? on Mon, 11 Mar 2024 11:42:35 +0000
writes:
> > > 
> > > ??? > Hi Martin
> > > ??? > Probably not the answer you're looking for but on
the
> > > latest
> > > Fedora 39 (workstation edition) both locally, and on a freshly
> > > installed VM (with just R-core installed), all fonts render
> > > correctly
> > > for me in evince.
> > > 
> > > ??? > $ evince --version
> > > ??? > GNOME Document Viewer 45.0
> > > 
> > > ??? > $ R --version
> > > ??? > R version 4.3.3 (2024-02-29) -- "Angel Food
Cake"
> > > ??? > Copyright (C) 2024 The R Foundation for Statistical
> > > Computing
> > > ??? > Platform: x86_64-redhat-linux-gnu (64-bit)
> > > 
> > > ??? > It may be worth sharing more details about your
> > > installation
> > > (e.g. Fedora version) to see if anyone has any ideas.
> > > 
> > > ??? > Tim
> > > 
> > > Thank you, Tim.
> > > 
> > > 
> > > Fedora is 38 :
> > > 
> > > $ lsb_release -a
> > > LSB Version:? :core-5.0-amd64:core-5.0-noarch:cxx-5.0-amd64:cxx-
> > > 5.0-noarch:desktop-5.0-amd64:desktop-5.0-noarch:languages-5.0-
> > > amd64:languages-5.0-noarch:printing-5.0-amd64:printing-5.0-noarch
> > > Distributor ID:? ? ? ?Fedora
> > > Description:? Fedora release 38 (Thirty Eight)
> > > Release:? ? ? 38
> > > Codename:? ? ?ThirtyEight
> > > 
> > > $ evince --version
> > > GNOME Document Viewer 44.3
> > > 
> > > R version does not matter at all.
> > > Same phenomenon in several versions of R I have installed
> > > simultaneously (from source).
> > > As I mentioned, I'm slightly misusing the list for non-R
problem
> > > that I encounter a lot with R? {because I like to use
> > > "plotmath"}, so I apologize in advance.
> > > 
> > > Maybe it's rather a matter of fonts installed in
> > > /usr/share/fonts/ ??
> > > 
> > > Martin
> > > 
> > > ??? > On Mon, 11 Mar 2024, at 10:51 AM, Martin Maechler wrote:
> > > ??? >> This problem has bugged me for several years now,
> > > ??? >> and our own IT staff has tried a few things, but
then
> > > never
> > > ??? >> cared enough to persist fixing it.
> > > ??? >> 
> > > ??? >> It *is* a bug in evince, the standard pdf viewer on
Fedora
> > > and
> > > ??? >> IIUC also quite few other Linux distributions, and
> > > ??? >> *not* a bug in R;? hence I am asking for help/hints
here.
> > > ??? >> 
> > > ??? >> A very simple example:
> > > ??? >> 
> > > ??? >>
----------------------------------------------------------
> > > ----
> > > -----------------
> > > ??? >> 
> > > ??? >> (pdfil <- paste0("plotmath-example_R",
> > > ??? >> with(R.version, paste0(major, sub("[.]",
"", minor))),
> > > ".pdf"))
> > > ??? >> ## "plomath-example_R433.pdf"
> > > ??? >> 
> > > ??? >> pdf(pdfil)
> > > ??? >> example(plotmath); mtext(R.version.string)
> > > ??? >> dev.off()
> > > ??? >> 
> > > ??? >> if(interactive())
> > > ??? >> system(paste("evince", pdfil,
"&"))
> > > ??? >> 
> > > ??? >>
----------------------------------------------------------
> > > ----
> > > -----------------
> > > ??? >> 
> > > ??? >> The pdf contains 4 pages, and in all of them *some*
of the
> > > math
> > > ??? >> symbols are replaced by open rectangles -- because
evince
> > > does
> > > ??? >> not find the fonts it should.
> > > ??? >> 
> > > ??? >> E.g.
> > > ??? >> - page 1: \pi is properly shown,? \phi not
> > > ??? >> - page 2: all greek letters,? \theta, \xi, \eta? are
*not*
> > > shown
> > > ??? >> ...
> > > ??? >> 
> > > ??? >> Simply typing
> > > ??? >> 
> > > ??? >> example(plotmath)
> > > ??? >> 
> > > ??? >> in the R console will show you everything as it
should be
> > > but
> > > is
> > > ??? >> not for us, using evince.
> > > ??? >> 
> > > ??? >> However, *everything* is rendered correctly, if I
use very
> > > old
> > > ??? >> 'xpdf' {which you may have to install
> > > ??? >> 
> > > ??? >> ## OTOH: This always work fine with the very old?
'xpdf' :
> > > ??? >> system(paste("xpdf", pdfil,
"&"))
> > > ??? >> 
> > > ??? >> So the fonts *are* somewhere on my machine, but
evince
> > > does
> > > not
> > > ??? >> find them;
> > > ??? >> 
> > > ??? >> How should our IT people fix this?
> > > ??? >> 
> > > ??? >> IIRC they did install the Zapf Dingbats fonts --
which
> > > then
> > > are
> > > ??? >> found by xpdf but not by evince ?
> > > ??? >> 
> > > ??? >> 
> > > ??? >> Thank you in advance,
> > > ??? >> Martin
> > > ??? >> 
> > > ??? >> _______________________________________________
> > > ??? >> R-SIG-Fedora mailing list
> > > ??? >> R-SIG-Fedora at r-project.org
> > > ??? >> https://stat.ethz.ch/mailman/listinfo/r-sig-fedora
> > > ??? >> 
> > > 
> > > ??? > [[alternative HTML version deleted]]
> > > 
> > > _______________________________________________
> > > R-SIG-Fedora mailing list
> > > R-SIG-Fedora at r-project.org
> > > https://stat.ethz.ch/mailman/listinfo/r-sig-fedora
> > 
> > _______________________________________________
> > R-SIG-Fedora mailing list
> > R-SIG-Fedora at r-project.org
> > https://stat.ethz.ch/mailman/listinfo/r-sig-fedora
> 
> 
> -- 
> I?aki ?car

	[[alternative HTML version deleted]]

Hi

I don't think this is an R issue (it is separate from the Cairo Symbol 
font problem).

For PDF output, R actually relies on the Symbol font having the Adobe 
Symbol Encoding (Appendix D of the PDF Reference 
https://opensource.adobe.com/dc-acrobat-sdk-docs/pdfstandards/pdfreference1.7old.pdf)
and just outputs the font as "Symbol", which relies on it being one of
the Standard 14 Fonts ...

"These fonts have built-in encodings that are unique to each
font."

... and ...

"These fonts, or their font metrics and suitable substitution fonts, 
must be available to the consumer application."

In other words, R passes the buck to the viewer to either have access to 
the Adobe Symbol font or use a substitute that has all of the necessary 
glyphs (and in that case, presumably to also take care of satisfying the 
Adobe Symbol Encoding).

It is possible for the R user to specify a different font name for the 
symbol font for PDF output, but that font has to have all of the 
necessary glyphs and it has to follow the Adobe Symbol Encoding or all 
bets are off.

Paul

On 12/03/24 06:59, I?aki Ucar wrote:
> Martin, I wouldn't rule out an R issue yet. Fonts are... tricky. So
I'm
> cc'ing Paul Murrell here.
> 
> I tried several?viewers here and I see the following: Chrome, Firefox 
> and Libreoffice Draw show the symbols; however, evince, okular and 
> xournal++ agree on **not** showing the symbols. **If** there is a bug, 
> the bug would be in fontconfig, because these ones AFAIK properly 
> delegate on fontconfig, which is the system-wide component that decides 
> what font substitution should be made for any given font. However, I see:
> 
> $ fc-match Helvetica
> NimbusSans-Regular.otf: "Nimbus Sans" "Regular"
> 
> which is the right choice. And okular confirms this by showing in a 
> properties dialog that it is substituting Helvetica with URW's Nimbus 
> Sans Regular. So why aren't the symbols displayed? My best guess is
that
> this has something to do with how R encodes such symbols. Paul 
> introduced some changes to fix similar issues for Cairo devices when 
> Fedora dropped support for Type 1 fonts, see [1]. Now, I'm no font 
> expert, but it seems to me that the pdf device may require similar 
> fixes. (And why do xpdf or Firefox show the glyphs... I have no idea. I 
> guess they do their?thing without asking fontconfig).
> 
> [1] 
>
https://blog.r-project.org/2020/04/17/changes-to-symbol-fonts-for-cairo-graphics-devices/
<https://blog.r-project.org/2020/04/17/changes-to-symbol-fonts-for-cairo-graphics-devices/>
> 
> Peter, as an aside, note that cairo_pdf embeds the fonts by default.
> 
> Best,
> I?aki
> 
> On Mon, 11 Mar 2024 at 15:31, <pstils at gmail.com 
> <mailto:pstils at gmail.com>> wrote:
> 
>     Hi Martin and Tim,
> 
>     I also have this bug. Though I think not necessarily with all the same
>     fonts as Martin.
> 
>     Using Martin's code:
> 
>     https://imgur.com/a/ILUoe3H
>     <https://imgur.com/a/ILUoe3H>
> 
>     Fedora 39, Evince 45.0
> 
>     It's a bug with Evince. I think. I think it's substituting in a
font
>     set that doesn't have all the required symbols. I think it should
be
>     possible to install the required fonts, but I haven't found a
solution
>     that way, yet.
> 
>     Nevertheless, the following should work, and may be a better solution
>     anyway, given that embedding the fonts is probably more cross-
>     platform/viewer friendly:
> 
> 
>     You can embed the fonts if you have Ghostscript installed (I think it
>     comes with Fedora already(?) if not then:
> 
>     sudo dnf install ghostscript
> 
>     )
> 
> 
>     You can then use the embedFonts() function in R:
> 
>     (pdfil <- paste0("plotmath-example_R",
>      ? ? ? ? ? ? ? ? ?with(R.version, paste0(major, sub("[.]",
"", minor))),
>     ".pdf"))
> 
>     pdf(pdfil)
>     example(plotmath); mtext(R.version.string)
>     dev.off()
> 
>     # Use embedFonts to embed the fonts in the PDF
>     embedFonts(file = pdfil, outfile = paste0("embedded-example",
pdfil),
>     options = "-dPDFSETTINGS=/prepress")
> 
> 
>     if(interactive()) {
>      ? system(paste("evince",
paste0("embedded-example", pdfil), "&"))
>     }
> 
> 
> 
>     Or you can do it in the terminal:
> 
> 
>     gs -dNOPAUSE -dBATCH -dPDFSETTINGS=/prepress -sDEVICE=pdfwrite -
>     dEmbedAllFonts=true -sOutputFile=plotmath-example-output_embedded.pdf -
>     f plotmath-example_R432.pdf
> 
> 
>     Compare:
> 
> 
>     Embedded:
> 
>     ? pdffonts plotmath-example-output_embedded.pdf
>     name? ? ? ? ? ? ? ? ? ?type? ? ?encoding emb sub uni object ID
>     ---------------------- -------- -------- --- --- --- ------ ---
>     KHEPSB+Helvetica? ? ? ?Type 1C? Custom? ?yes yes no? ? ? 10? ?0
>     WNPVSJ+Symbol? ? ? ? ? Type 1C? Custom? ?yes yes no? ? ? 12? ?0
>     MQBKOK+Helvetica-Bold? Type 1C? WinAnsi? yes yes no? ? ? 20? ?0
> 
> 
>     Original:
> 
>     ? pdffonts plotmath-example_R432.pdf
>     name? ? ? ? ? ? ? ? ? ?type? ? ?encoding emb sub uni object ID
>     ---------------------- -------- -------- --- --- --- ------ ---
>     Helvetica? ? ? ? ? ? ? Type 1? ?Custom? ?no? no? no? ? ? 16? 0
>     Helvetica-Bold? ? ? ? ?Type 1? ?Custom? ?no? no? no? ? ? 17? 0
>     Symbol? ? ? ? ? ? ? ? ?Type 1? ?Symbol? ?no? no? no? ? ? 18? 0
> 
> 
>     I hope this works for you. Like I said, I *think* it's a problem
with
>     Evince so it's probably better to file a bug report with them, but
I
>     also think embedding fonts isn't such a bad idea anyway -
you'll know
>     the output will display as intended regardless of the viewer on the
>     user's system. It does lead to a larger file-size, but I think
these
>     days we can live with that.
> 
>     Thanks,
>     Peter
> 
> 
> 
> 
>     On Mon, 2024-03-11 at 14:15 +0100, Martin Maechler wrote:
>      > > > > > > Tim Taylor
>      > > > > > > ??? on Mon, 11 Mar 2024 11:42:35 +0000
writes:
>      >
>      > ??? > Hi Martin
>      > ??? > Probably not the answer you're looking for but on
the latest
>      > Fedora 39 (workstation edition) both locally, and on a freshly
>      > installed VM (with just R-core installed), all fonts render
correctly
>      > for me in evince.
>      >
>      > ??? > $ evince --version
>      > ??? > GNOME Document Viewer 45.0
>      >
>      > ??? > $ R --version
>      > ??? > R version 4.3.3 (2024-02-29) -- "Angel Food
Cake"
>      > ??? > Copyright (C) 2024 The R Foundation for Statistical
Computing
>      > ??? > Platform: x86_64-redhat-linux-gnu (64-bit)
>      >
>      > ??? > It may be worth sharing more details about your
installation
>      > (e.g. Fedora version) to see if anyone has any ideas.
>      >
>      > ??? > Tim
>      >
>      > Thank you, Tim.
>      >
>      >
>      > Fedora is 38 :
>      >
>      > $ lsb_release -a
>      > LSB Version:? :core-5.0-amd64:core-5.0-noarch:cxx-5.0-amd64:cxx-
>      > 5.0-noarch:desktop-5.0-amd64:desktop-5.0-noarch:languages-5.0-
>      > amd64:languages-5.0-noarch:printing-5.0-amd64:printing-5.0-noarch
>      > Distributor ID:? ? ? ?Fedora
>      > Description:? Fedora release 38 (Thirty Eight)
>      > Release:? ? ? 38
>      > Codename:? ? ?ThirtyEight
>      >
>      > $ evince --version
>      > GNOME Document Viewer 44.3
>      >
>      > R version does not matter at all.
>      > Same phenomenon in several versions of R I have installed
>      > simultaneously (from source).
>      > As I mentioned, I'm slightly misusing the list for non-R
problem
>      > that I encounter a lot with R? {because I like to use
>      > "plotmath"}, so I apologize in advance.
>      >
>      > Maybe it's rather a matter of fonts installed in
>      > /usr/share/fonts/ ??
>      >
>      > Martin
>      >
>      > ??? > On Mon, 11 Mar 2024, at 10:51 AM, Martin Maechler wrote:
>      > ??? >> This problem has bugged me for several years now,
>      > ??? >> and our own IT staff has tried a few things, but
then never
>      > ??? >> cared enough to persist fixing it.
>      > ??? >>
>      > ??? >> It *is* a bug in evince, the standard pdf viewer on
Fedora and
>      > ??? >> IIUC also quite few other Linux distributions, and
>      > ??? >> *not* a bug in R;? hence I am asking for help/hints
here.
>      > ??? >>
>      > ??? >> A very simple example:
>      > ??? >>
>      > ??? >>
--------------------------------------------------------------
>      > -----------------
>      > ??? >>
>      > ??? >> (pdfil <- paste0("plotmath-example_R",
>      > ??? >> with(R.version, paste0(major, sub("[.]",
"", minor))),
>      > ".pdf"))
>      > ??? >> ## "plomath-example_R433.pdf"
>      > ??? >>
>      > ??? >> pdf(pdfil)
>      > ??? >> example(plotmath); mtext(R.version.string)
>      > ??? >> dev.off()
>      > ??? >>
>      > ??? >> if(interactive())
>      > ??? >> system(paste("evince", pdfil,
"&"))
>      > ??? >>
>      > ??? >>
--------------------------------------------------------------
>      > -----------------
>      > ??? >>
>      > ??? >> The pdf contains 4 pages, and in all of them *some*
of the
>      > math
>      > ??? >> symbols are replaced by open rectangles -- because
evince does
>      > ??? >> not find the fonts it should.
>      > ??? >>
>      > ??? >> E.g.
>      > ??? >> - page 1: \pi is properly shown,? \phi not
>      > ??? >> - page 2: all greek letters,? \theta, \xi, \eta? are
*not*
>      > shown
>      > ??? >> ...
>      > ??? >>
>      > ??? >> Simply typing
>      > ??? >>
>      > ??? >> example(plotmath)
>      > ??? >>
>      > ??? >> in the R console will show you everything as it
should be but
>      > is
>      > ??? >> not for us, using evince.
>      > ??? >>
>      > ??? >> However, *everything* is rendered correctly, if I
use very old
>      > ??? >> 'xpdf' {which you may have to install
>      > ??? >>
>      > ??? >> ## OTOH: This always work fine with the very old?
'xpdf' :
>      > ??? >> system(paste("xpdf", pdfil,
"&"))
>      > ??? >>
>      > ??? >> So the fonts *are* somewhere on my machine, but
evince does
>      > not
>      > ??? >> find them;
>      > ??? >>
>      > ??? >> How should our IT people fix this?
>      > ??? >>
>      > ??? >> IIRC they did install the Zapf Dingbats fonts --
which then
>      > are
>      > ??? >> found by xpdf but not by evince ?
>      > ??? >>
>      > ??? >>
>      > ??? >> Thank you in advance,
>      > ??? >> Martin
>      > ??? >>
>      > ??? >> _______________________________________________
>      > ??? >> R-SIG-Fedora mailing list
>      > ??? >> R-SIG-Fedora at r-project.org
<mailto:R-SIG-Fedora at r-project.org>
>      > ??? >> https://stat.ethz.ch/mailman/listinfo/r-sig-fedora
>     <https://stat.ethz.ch/mailman/listinfo/r-sig-fedora>
>      > ??? >>
>      >
>      > ??? > [[alternative HTML version deleted]]
>      >
>      > _______________________________________________
>      > R-SIG-Fedora mailing list
>      > R-SIG-Fedora at r-project.org <mailto:R-SIG-Fedora at
r-project.org>
>      > https://stat.ethz.ch/mailman/listinfo/r-sig-fedora
>     <https://stat.ethz.ch/mailman/listinfo/r-sig-fedora>
> 
>     _______________________________________________
>     R-SIG-Fedora mailing list
>     R-SIG-Fedora at r-project.org <mailto:R-SIG-Fedora at
r-project.org>
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>     <https://stat.ethz.ch/mailman/listinfo/r-sig-fedora>
> 
> 
> 
> -- 
> I?aki ?car
-- 
Dr Paul Murrell (he/him)
Te Kura Tatauranga | Department of Statistics
Waipapa Taumata Rau | The University of Auckland
Private Bag 92019, Auckland 1142, New Zealand
64 9 3737599 x85392
paul at stat.auckland.ac.nz
www.stat.auckland.ac.nz/~paul/